Aligments for a candidate for thrC in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for thrC in Escherichia coli BW25113

Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate 14149 b0004 threonine synthase (NCBI)

Query= CharProtDB::CH_002114
         (428 letters)



>lcl|FitnessBrowser__Keio:14149 b0004 threonine synthase (NCBI)
          Length = 428

 Score =  851 bits (2199), Expect = 0.0
 Identities = 428/428 (100%), Positives = 428/428 (100%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS
Sbjct: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
           AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH
Sbjct: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120

Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180
           IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV
Sbjct: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180

Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240
           AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ
Sbjct: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240

Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300
           LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA
Sbjct: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300

Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360
           MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA
Sbjct: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360

Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420
           LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL
Sbjct: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420

Query: 421 RKLMMNHQ 428
           RKLMMNHQ
Sbjct: 421 RKLMMNHQ 428


Lambda     K      H
   0.319    0.135    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 773
Number of extensions: 19
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 428
Length of database: 428
Length adjustment: 32
Effective length of query: 396
Effective length of database: 396
Effective search space:   156816
Effective search space used:   156816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 14149 b0004 (threonine synthase (NCBI))
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00260.hmm
# target sequence database:        /tmp/gapView.27944.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.6e-134  434.3   0.0   1.9e-134  434.1   0.0    1.0  1  lcl|FitnessBrowser__Keio:14149  b0004 threonine synthase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14149  b0004 threonine synthase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.1   0.0  1.9e-134  1.9e-134       1     339 [.      52     397 ..      52     398 .. 0.97

  Alignments for each domain:
  == domain 1  score: 434.1 bits;  conditional E-value: 1.9e-134
                       TIGR00260   1 vvryreilevt...ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnetv 76 
                                     v+r+++il+++   e++++ l+e+++++f++p++ ++v++ ++ ++elfhgPtlaFKD+g++f+a++lt++++++  t+
  lcl|FitnessBrowser__Keio:14149  52 VTRSAKILSAFigdEIPQEILEERVRAAFAFPAPVANVES-DVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTI 129
                                     689999999999999*************************.************************************** PP

                       TIGR00260  77 lcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...klkl 152
                                     l+AtsGdtgaa+a+a++g +nvkvv+LyP+gkisp++ekl+++l +n++++ai+GdFD++q+lvk++f+d+e   +l+l
  lcl|FitnessBrowser__Keio:14149 130 LTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEElkvALGL 208
                                     *********************************************************************777777**** PP

                       TIGR00260 153 nsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflks 231
                                     ns+Nsin++r++aq++y+fe+v+ql++e+++++vv+vpsgnfg++++G l +k+lglp  k++iaa++++d+v+rfl++
  lcl|FitnessBrowser__Keio:14149 209 NSANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAG-LLAKSLGLP-VKRFIAATNVNDTVPRFLHD 285
                                     ************************************************.7788888**.99****************** PP

                       TIGR00260 232 gdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkkl 310
                                     g+++pk++++Tls+Amd+++p+n++r++el+rr+ ++l++l+++++d+e+++++++ ++e gy+ eph+ava++al+++
  lcl|FitnessBrowser__Keio:14149 286 GQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRALRDQ 364
                                     ******************************************************************************* PP

                       TIGR00260 311 vekgvs....atadpaKFeevvealtgnklkdp 339
                                     ++ g +    +ta+paKF+e+vea++g++l+ p
  lcl|FitnessBrowser__Keio:14149 365 LNPGEYglflGTAHPAKFKESVEAILGETLDLP 397
                                     ****555889*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (428 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.10
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis